redOrbit Staff & Wire Reports – Your Universe Online
In a development expected to improve the process of matching organ donors and understanding how genes contribute to diseases, researchers have devised a method that can help determine whether or not a specific genetic sequence came from an individual’s mother or father.
The technique, which was developed by experts from the Ludwig Institute for Cancer Research and is described in the latest edition of the journal Nature Biotechnology, helps address a longstanding challenge when it comes to genome sequencing – discovering which traits come from which parent. The authors believe that the technique could improve personalized medicine.
“The technique will enable clinicians to better assess a person’s individual risk for disease. It is potentially transformative for personalized medicine,” explained Bing Ren, a Ludwig scientist working at the University of California, San Diego School of Medicine. “Current sequencing technologies are fast and rapidly getting cheaper… in the not too distant future, everyone’s genome will be sequenced. That will become the standard of care.”
However, Ren said, there is a potential issue with that scenario. With the exception of sex chromosomes, each person has two copies of each chromosome – one copy coming from their mother, and the other from their father. Current sequencing technology cannot distinguish between the two copies of each gene, and thus have difficulty determining whether particular genetic differences originate with a person’s mom or dad.
That’s where the new technique, HaploSeq, comes in. HaploSeq is described by the study authors as a mixture of molecular and computational biology, and allows researchers to determine which genetic variants occur together on the same stretch of a chromosome. That knowledge can tell whether or not the variations came from the same patent, and that discovery will have “profound effects on genetic research and discovery,” according to Siddarth Selvaraj, a member of the research team from UC San Diego.
“More immediately, the technique will enable clinicians to better assess a person’s individual risk for disease, a cornerstone of personalized medicine,” the Ludwig Institute said in a statement Sunday. “For instance, people at risk for a disease such as cancer often have more than one DNA mutation. HaploSeq could enable clinicians to determine if the two mutations are on the same chromosome or on different chromosomes, which can help in risk assessment – for instance, risk may be reduced if two mutations are on the same chromosome.”
In addition, with some additional fine-tuning, the technique could also streamline the process of finding a genetic match between an organ donor and the patient in need of the transplant. A large number of genes contribute to donor-recipient compatibility, the authors note. However, there is a lot of genetic variability in those genes, and the HaploSeq method could lead to the creation of a DNA database that would make it easier to determine whether or not a donor would be a good genetic match to a patient in need of an organ transplant.
“In principal, you could compare your genetic sequence to your neighbor’s and ask if you have any recent ancestors in common,” Ren said. “With our technique we can study each individual and how they relate to other individuals. As we accumulate data from many individuals we can more precisely determine their relationships… I anticipate that this new method will be quite widely used.”